The new E. coli?

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When I first started research as an undergraduate, a research assistant told me that my days would be variations on the theme, 'hurry up and wait.' I had no concept of what this meant until I started wading through the lab protocols: set up PCR and WAIT; load the DNA gel and WAIT; cut the DNA, WAIT; ligate and WAIT; and then finally transform E. coli and then go home because it would take about 18 hours to get a colony to screen. You've worked the whole day you've got nothing corporeal to show for it, only a a blank petri plate and waste bucket full of Eppendorfs.

And then for some reason I went on to study mycobacteria (some would say masochism; I wouldn't argue), where TB colonies and cultures take weeks to come up (if at all). Even my preferred mycobacteria, our powerhouse M. smegmatis with an awesome doubling time of 3 hours still took 3 days to get colonies. A full week to go from promising hypothesis to inconclusive result. Many a daydreams revolved around finding that magic switch that could turn 'smeg' into E. coli so that I could actually go test the gamut of random, backlogged ideas I had.

In my postdoc, I switched to Vibrio cholerae, which had a doubling time under 20 minutes and beat E. coli handily to stationary phase. But I didn't really 'get' what it meant to have that fast a turnaround time until I was standing in our odorous warm room, rather gobsmacked the first time I saw colonies appearing on my V. cholerae transformation plates that I had done that same morning. Suddenly, I could hope to get cloning and culturing done in a single day and fast track my way to running the actual experiments I cared about. And at the same time, it was amazing to appreciate just how much of our time we invest in waiting for our strains to grow.

This is the argument of George Church and colleagues in a recent paper on bioRxiv for finding a new bacterial host for making genetic constructs. In their work, they identify and sequence Vibrio natriegens, a non-pathogenic, marine Gram negative with a doubling time as fast as 10 minutes. They argue, as covered in Science, that such a fast turnaround time (transformation to colony in 5 hours) could significantly reduce the time investment in more mundane aspects of research and thus improve productivity.

But before we all start throwing out our Top10 and BL21 cells and relegate E. coli K12 to the dustbin of history, there is a lot of optimization that remains to make V. natriegens a true workhorse in the lab. Currently, transformation rates are around 10^5 CFU per ug DNA, a drop of up to 5 logs compared to commercialized E. coli cloning strains. The authors also found that transposition using a Mariner-based transposon was not as diverse as was found with similar protocols in E. coli, though Cas9 mediated gene inactivation was successful.

Beyond the biotech applications, one point that the discovery of V. natriegens highlights is just how little we really know about why different bacteria have such disparate replication times (from minutes to days).

Is it that our standard medias are suboptimal for various bacteria? Or is it intrinsic? Are there growth restraining factors programmed to reduce growth even in 'optimal conditions' (and if so, why is this selected for)? And how do these mechanisms work (and can we make TB into the new E. coli, er V. natriegens)?

So, is E. coli K12 done for in the lab? No, because fast growth doesn't become revolutionary until the vast array of other tools now currently available for E. coli including mutant libraries can be translated into other species. So the crown remains comfortably snug around E. coli's piliated head. But, as we explore the diversity of the natural world, it should consider hiring a security detail, just in case.

I first developed an interest in bacterial pathogenesis while at Cornell University. I then earned my PhD in Biomedical and Biological Sciences from Harvard University in Eric Rubin’s laboratory, studying cell wall remodelling in Mycobacterium tuberculosis. From 2012-2015, I continued my training as a postdoctoral fellow in Matthew Waldor’s lab at Harvard Medical School, investigating the role of DNA methylation on regulating fundamental cellular processes in Vibrio cholerae.

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